The Congressional Budget Office said the F.D.A. would need a total of $580 million from 2011 to 2015 to carry out the changes required by the Food Safety Modernization Act. So far, Congress has appropriated less than half of that amount, even as the agency is moving to issue crucial rules under the law this year.

“I don’t think it’s too much to say that the success” of the overhaul “is on the line,” Michael R. Taylor, the deputy F.D.A. commissioner for foods and veterinary medicine, said in an interview. “We have good plans for moving forward. The problem is we don’t have the money.”

An estimated 48 million Americans have food-borne illnesses each year, and agency officials say the funding shortfall could undermine Congress’s intent to make the most significant improvements to the food safety system in more than 70 years.

Representative Rosa DeLauro, a Connecticut Democrat who helped write the law, said the White House and the Department of Health and Human Services, the parent agency of the F.D.A., shared some of the blame for the shortfall because they had tried to impose user fees on the food industry to help fund the law. The F.D.A. relies on user fees for a number of other programs.

In its previous five budget requests, the F.D.A. proposed user fees that would cover the bulk of the cost of carrying out the food safety law. Last year, for example, it asked for $263 million for the law, with about $229 million coming from fees on food companies.

But lawmakers soundly rejected those proposals after lobbying by the food industry.

Ms. DeLauro helped write a letter last year asking the Obama administration to request the necessary funding through a federal appropriation. “User fees are a nonstarter,” she said in an interview. “They are just not going to get through Congress.”

After receiving an appropriation of $27.5 million for the law in the current fiscal year, the F.D.A. asked Congress to allocate $109.5 million for the coming year. But it remains to be seen if the Republican-led Congress, given the mood for cutting spending, will approve the higher amount. Even if the agency receives it, the figure would be just half of what the budget office says is necessary.

“If we keep shortchanging the F.D.A., it will continue to cost us billions of dollars a year to deal with food-borne illness,” said Ms. DeLauro, a member of the appropriations subcommittee that oversees the agency’s funding.

The food safety law puts the burden on food companies to make sure that their products are safe, instead of relying largely on inspectors from the understaffed F.D.A. It requires better record-keeping, contingency plans for handling outbreaks and measures to prevent the spread of contaminants. It also gives the agency the power to issue recalls, something it could not do previously.

Consumer groups have accused the Obama administration of being slow to move the rules through the regulatory process. They sued in 2012 to force the F.D.A. to accelerate its timetable on issuing final rules. A settlement was reached last year, and the agency will publish some of the final regulations this year.

Mr. Taylor, the F.D.A. official, said that the agency had been able to issue new rules, including those for produce and processed foods, but that funding shortfalls would make it difficult to modernize its inspection processes and retrain about 2,000 inspectors and other staff members for the new requirements.

He also said that the agency would have problems providing guidance and technical assistance to the states, which conduct inspections under contract with the F.D.A. In addition, he said, it will be difficult for the agency to properly oversee food imports.

“If they don’t have the capacity to enforce it, the law is not going to be worth the paper it’s written on,” said Tony Corbo, a lobbyist for Food & Water Watch, a consumer group.

At a hearing on the F.D.A.’s budget last month, Representative Harold Rogers, Republican of Kentucky and chairman of the House Appropriations Committee, said that he was concerned about the size of the agency’s overall budget request and that the request for more than $100 million for the food safety law “will be tough to swallow.”

According to the Centers for Disease Control and Prevention, about 128,000 people are hospitalized each year with food-related illnesses, and 3,000 die. The cost of treatment and lost income is $15 billion a year or more, according to data from the Agriculture Department.

The food safety law is intended to change the F.D.A.’s inspection system, which critics say provides inadequate oversight of the billions of pounds of food produced and eaten each year. The food safety system is spread out over more than 15 agencies, but the F.D.A. is responsible for the bulk of what Americans eat.

Under the law, the agency is supposed to increase its inspections of foreign food facilities that export to the United States. But a report by the Government Accountability Office found that the agency had not kept up with the pace of inspections mandated by Congress.

Lawmakers required the F.D.A. to inspect 600 foreign food plants in the first year after the measure was passed. In each of the next five years, the agency was supposed to inspect at least twice the number of facilities reviewed the previous year. It should have inspected at least 4,800 facilities in 2014, according to the accountability office, but it inspected only 1,323.

The office also noted that the F.D.A. continued to have problems filling staff positions that were supposed to help with the oversight of foreign food plants.

Despite the funding shortfalls, some food safety advocates say they are optimistic that Congress will ultimately give the agency the money it needs to protect consumers and modernize a food safety system that has been in place for nearly a century.

“Is the funding request enough? No,” said Colin O’Neil, the director of government affairs for the Center for Food Safety, one of the groups that sued the F.D.A. “But it gets us on the way. It’s going to be a long fight. But I think we will get there.”

A version of this article appears in print on , on Page A12 of the New York edition with the headline: Law Aims to Prevent Food-Borne Illnesses, but Funding From Congress Falls Short. Order Reprints | Today’s Paper | Subscribe